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I have recently started to replay this game, and I have a dim recollection that there are several glitches in the research tree, such that if you research the wrong thing first, you could end up in a situation where you can't research what you need to complete the game. Is there a complete list of all of these glitches?

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There looks to be a full discussion on this page from UFOPaedia. A basic recap is

Glitches in the System

There are two major occasions where research can grind to a halt:

  • An alien is required to further research AFTER certain projects are completed

  • An object is needed in storage before research is completed

So if X is a trigger to unlock some new research, but it also requires A and B, you need to make sure that you have A and B when you complete X. Otherwise, you may need to complete X again (in the case of interrogations) or be stuck completely in some cases.

The page lists all the places where you can get stuck and how to avoid it.

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The single biggest glitch involves the order of the live Deep One terrorist. Make sure not to research this until you have researched a dead Deep One, Aqua-Plastic Armor, and for good measure, all of the sub components. Assuming you've researched all of those, you are clear to research the Live Deep One.

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Once you start getting lobster man in terror sites (the only place where you can get a deep one) there won't be anymore deep ones coming anymore (or maybe if you lucky). The other answers describe why a deep man is so important so make sure you capture one and keep him alive as soon as possible. You will not be able to continue more advanced research without one.

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